I have given this some thought and here is what I have come up with for some house rules for skills. This is only a rough draft and feedback is welcome from interested players and those who are just interested in watching the campaign or feel they have something constructive to add.
Synergy
I like simplicity. I also do not like to encourage optimizing skills by taking only 5 ranks just to get the synergy. Therefore, there are no synergy bonuses.
Appraise
The ability to determine the value of items as well as to differentiate the wheat from the chaff is quite useful to adventurers. So the uses for this skill are expanded.
Check: You can determine the approximate value of various items in an area simply by making a few cursory glances. Common items are those which are non-magical in nature and generally worth 50 gp or less. Valuable items are those which are either of masterwork quality or made by a master craftsman or artificer. It can also include raw materials or ingredients for more powerful items, such as reagents to create magical items, as well as common magical items such as a potion of cure light wounds or a feather fall talisman. Valuable items are generally worth 500 gp or less, although there are exceptions, such as full plate armor. Rare items are those which are worth a great deal, often thousands of gold pieces and may not appear to have value at first glance, although a trained eye can pick them out.
The DC for common items is 12, the DC for valuable items is 15, and the DC for rare items is 20. After examining an area, a character is able to pick out any items and identify their general type for any DCs he surpassed, although determining their actual value takes more careful inspection.
Action: Examining an area takes one full-round action for each 10-foot square area. An entire room can be examined with a single check. The only difference is the amount of time based on the size of the room.
Rules for appraising individual items are unchanged.
Bluff
I believe this skill works well as written for the most part. However, in order to reduce meta-gaming, whenever an NPC attempts to lie, I will roll the NPC's Bluff check and compare it to the PC's Sense Motive score + 10. This will be the PC's Passive Sense Motive score. If the NPC fails, then the PC will pick up on some tell that indicates the NPC is lying, such as shuffling of the feet or looking away while talking. PCs roll Bluff checks normally. I will determine what requires a Bluff check and what does not.
Diplomacy
Whenever you are introduced to an NPC for the first time, you may make a Diplomacy check to determine that NPC's starting attitude. However, I will add +1 to the DC for every level or hit die of the NPC to determine the outcome. Use of the skill for this purpose is optional and merely represents your character trying to make a good impression on the NPC, much like reaction checks in 1st and 2nd edition.
The primary use of the Diplomacy skill will be to persuade NPCs to accept a proposal, and will follow Rich Burlew's modified Diplomacy skill below with a couple modifiers removed as I feel they were superfluous:
Use this skill to ask the local baron for assistance, to convince a band of thugs not to attack you, or to talk your way into someplace you aren't supposed to be.
Check: You can propose a trade or agreement to another creature with your words; a Diplomacy check can then persuade them that accepting it is a good idea. Either side of the deal may involve physical goods, money, services, promises, or abstract concepts like "satisfaction." The DC for the Diplomacy check is based on three factors: who the target is, the relationship between the target and the character making the check, and the risk vs. reward factor of the deal proposed.
The Target: The base DC for any Diplomacy check is equal to the 15 + level of the highest-level character in the group that you are trying to influence + the Wisdom modifier of the character in the group with the highest Wisdom. High-level characters are more committed to their views and are less likely to be swayed; high Wisdom characters are more likely to perceive the speaker's real motives and aims. By applying the highest modifiers in any group, a powerful king (for example) might gain benefit from a very wise advisor who listens in court and counsels him accordingly. For this purpose, a number of characters is only a "group" if they are committed to all following the same course of action. Either one NPC is in charge, or they agree to act by consensus. If each member is going to make up their mind on their own, roll separate Diplomacy checks against each.
The Relationship: Whether they love, hate, or have never met each other, the relationship between two people always influences any request.
-10 Intimate: Someone who with whom you have an implicit trust. Example: A lover or spouse.
-5 Ally: Someone on the same team, but with whom you have no personal relationship. Example: A cleric of the same religion or a knight serving the same king.
+0 Just Met: Someone with whom you have no relationship or someone you have met several times with no particularly positive or negative experiences. Example: A guard at a castle or a traveler on a road.
+5 Enemy: Someone on an opposed team, with whom you have no personal relationship. Example: A cleric of a philosophically-opposed religion or an orc bandit who is robbing you.
+10 Nemesis: Someone who has sworn to do you, personally, harm. Example: The brother of a man you murdered in cold blood.
Risk vs. Reward Judgement: The amount of personal benefit must always be weighed against the potential risks for any deal proposed. It is important to remember to consider this adjustment from the point of view of the NPC themselves and what they might value; while 10 gp might be chump change to an adventurer, it may represent several months' earnings for a poor farmer. Likewise, a heroic paladin is unlikely to be persuaded from his tenets for any amount of gold, though he might be convinced that a greater good is served by the proposed deal. When dealing with multiple people at once, always consider the benefits to the person who is in clear command, if any hierarchy exists within the group.
-10 Fantastic: The reward for accepting the deal is very worthwhile, and the risk is either acceptable or extremely unlikely. The best-case scenario is a virtual guarantee. Example: An offer to pay a lot of gold for something of no value to the subject, such as information that is not a secret.
-5 Favorable: The reward is good, and the risk is tolerable. If all goes according to plan, the deal will end up benefiting the subject. Example: A request to aid the party in battle against a weak goblin tribe in return for a cut of the money and first pick of the magic items.
+0 Even: The reward and risk are more or less even, or the deal involves neither reward nor risk. Example: A request for directions to someplace that is not a secret.
+5 Unfavorable: The reward is not enough compared to the risk involved; even if all goes according to plan, chances are it will end up badly for the subject. Example: A request to free a prisoner the subject is guarding (for which he or she will probably be fired) in return for a small amount of money.
+10 Horrible: There is no conceivable way the proposed plan could end up with the subject ahead, or the worst-case scenario is guaranteed to occur. Example: A offer to trade a bit of dirty string for a castle.
Success or Failure: If the Diplomacy check beats the DC, the subject accepts the proposal, with no changes or with minor (mostly idiosyncratic) changes. If the check fails by 5 or less, the subject does not accept the deal but may, at the DM's option, present a counter-offer that would push the deal up one place on the risk-vs.-reward list. For example, a counter-offer might make an Even deal Favorable for the subject. The character who made the Diplomacy check can simply accept the counter-offer, if they choose; no further check will be required. If the check fails by 10 or more, the Diplomacy is over; the subject will entertain no further deals, and may become hostile or take other steps to end the conversation.
Action: Making a request or proposing a deal generally requires at least 1 full minute. In many situations, this time requirement may greatly increase.
Try Again: If you alter the parameters of the deal you are proposing, you may try to convince the subject that this new deal is even better than the last one. This is essentially how people haggle. As long as you never roll 10 or less than the DC on your Diplomacy check, you can continue to offer deals.
Disguise
This skill is essentially unchanged when used by PCs, but as with the Bluff skill, when NPCs use it, they will make a roll against the PC's Passive Spot skill which is their Spot score +10.
Forgery
Documents are very important in Eberron. Having the right papers can mean the difference between a friendly chat and imprisonment. Consequently, the Forgery skill is incredibly useful in Eberron and has some expanded description in the Eberron Campaign Setting page 46. The Player's Guide to Eberron page 38 also lists many of the documents that are common in Eberron.
Gather Information
There are two uses of the Gather Information skill, general and specific. Trying to learn general information such as the latest news is typically DC 10 and takes 1d4+1 hours as usual. Some checks for general information do not take nearly so much time, such as asking for the nearest temple or inn when one does not care what type of temple or inn. These checks take only 1d4x10 minutes.
Specific information, such as the location of a particular named tavern or the estate of a certain noble has a DC of 15 and takes 1d4+1 hours, provided the information is commonly known.
There are several modifiers that might make Gathering Information more difficult. If the community is particularly insular, such as an elf asking questions in a goblin town, the DC is increased by 5. If the information is not generally well-known, the DC is likewise increased by 5, while for secret information the DC is increased by 10.
In Sharn, information is a commodity, and commodities always have a price. It costs 1 gp per point of the DC of a Gather Information check. This price is the same whether the check is successful or not.
Failure: If you fail a Gather Information check by 5 or more while asking around in an insular community, the DC increases by a further 5 points, but this increase only applies after the first failed check. If you fail a Gather Information check by 5 or more while seeking secret information, then you may alert someone who does not want the information to be known. That party may take hostile action against the PC making the check.
Hide
When used by NPCs, this skill works as the Bluff skill, above. The PC uses a Passive Spot equal to 10 + his Spot bonus.
Intimidate
This skill has the same purpose as Diplomacy. Only the means differ. The same modifiers for Relationship and Risk vs. Reward Judgment apply, but otherwise the mechanics are the same. Similarly, you may attempt to Intimidate an entire group as opposed to an individual, using the highest of the group's level or hit die, Wisdom bonus, and saves against fear.
Move Silently
See Hide. The PC uses a Passive Listen equal to 10 + his Listen bonus.
Sense Motive
A Hunch has a DC of 15 + the target's level or hit die + the target's Charisma modifier. This can be incredibly useful when trying to determine the motivation of NPCs during negotiations.
Unless an NPC is lying, all uses of this skill are active. So it is not necessary to roll a Sense Motive check to determine if an NPC is lying. I will make the roll secretly and inform you if you notice a tell. But if you wish to get a hunch, sense enchantment, or see if someone is sending a secret message, then you will need to actively roll a Sense Motive check.